Infection Class Reference

CPP API: mio::abm::Infection Class Reference

CPP API

#include <infection.h>

Collaboration diagram for mio::abm::Infection:

Public Member Functions
auto	default_serialize ()
	This method is used by the default serialization feature. More...

InfectionState	get_infection_state (TimePoint t) const
	Get the InfectionState of the Infection. More...

TimePoint	get_start_date () const

ScalarType	get_viral_load (TimePoint t) const
	Gets the ViralLoad of the Infection at a given TimePoint. More...

ScalarType	get_viral_shed (TimePoint t) const
	Get viral shed at a specific time. More...

VirusVariant	get_virus_variant () const
	: Get VirusVariant. More...

	Infection (PersonalRandomNumberGenerator &rng, VirusVariant virus, AgeGroup age, const Parameters &params, TimePoint init_date, InfectionState init_state, const InitialInfectionStateDistribution &init_state_dist, ProtectionEvent latest_protection={ProtectionType::NoProtection, TimePoint(0)}, bool detected=false)
	Create an Infection for a single Person with a time spent in the given initial state that is drawn from the given distribution. More...

	Infection (PersonalRandomNumberGenerator &rng, VirusVariant virus, AgeGroup age, const Parameters &params, TimePoint start_date, InfectionState start_state=InfectionState::Exposed, ProtectionEvent latest_protection={ProtectionType::NoProtection, TimePoint(0)}, bool detected=false)
	Create an Infection for a single Person. More...

bool	is_detected () const

void	set_detected ()
	Set the Infection to detected. More...

Private Member Functions
ScalarType	calculate_death_probability (AgeGroup age, const Parameters &params) const
	Calculate the overall death probability for the infection. More...

TimePoint	draw_infection_course_backward (PersonalRandomNumberGenerator &rng, AgeGroup age, const Parameters &params, TimePoint init_date, InfectionState init_state)
	Determine Infection course prior to the given InfectionState start_state. More...

void	draw_infection_course_forward (PersonalRandomNumberGenerator &rng, AgeGroup age, const Parameters &params, TimePoint init_date, InfectionState init_state, ProtectionEvent latest_protection)
	Determine Infection course subsequent to the given InfectionState start_state. More...

StateTransition	get_backward_transition (PersonalRandomNumberGenerator &rng, AgeGroup age, const Parameters &params, InfectionState current_state) const
	Get the backward transition from a given infection state. More...

StateTransition	get_dead_backward_transition (PersonalRandomNumberGenerator &rng, AgeGroup age, const Parameters &params) const
	Get the backward transition from dead state. More...

StateTransition	get_forward_transition (PersonalRandomNumberGenerator &rng, AgeGroup age, const Parameters &params, InfectionState current_state, TimePoint current_time, ProtectionEvent latest_protection) const
	Get the forward transition from a given infection state. More...

StateTransition	get_recovered_backward_transition (PersonalRandomNumberGenerator &rng, AgeGroup age, const Parameters &params) const
	Get the backward transition from recovered state. More...

ScalarType	get_severity_protection_factor (const Parameters &params, ProtectionEvent latest_protection, AgeGroup age, TimePoint current_time) const
	Get the severity protection factor based on latest protection. More...

	Infection ()=default

void	initialize_viral_load (PersonalRandomNumberGenerator &rng, VirusVariant virus, AgeGroup age, const Parameters &params, ProtectionEvent latest_protection)
	Initialize the viral load parameters for the infection. More...

void	initialize_viral_shed (PersonalRandomNumberGenerator &rng, VirusVariant virus, AgeGroup age, const Parameters &params)
	Initialize the viral shed parameters and individual factor for the infection. More...

Private Attributes
friend	DefaultFactory< Infection >

bool	m_detected
	Whether an Infection is detected or not. More...

ScalarType	m_individual_viral_shed_factor
	Individual viral shed factor. More...

std::vector< std::pair< TimePoint, InfectionState > >	m_infection_course
	Start date of each InfectionState. More...

ScalarType	m_log_norm_alpha

ScalarType	m_log_norm_beta
	Parameters for the viral shed mapping, which is modelled through an invlogit function. More...

ViralLoad	m_viral_load
	ViralLoad of the Infection. More...

VirusVariant	m_virus_variant
	Variant of the Infection. More...

Constructor & Destructor Documentation

◆ Infection() [1/3]

mio::abm::Infection::Infection	(	PersonalRandomNumberGenerator &	rng,
		VirusVariant	virus,
		AgeGroup	age,
		const Parameters &	params,
		TimePoint	start_date,
		InfectionState	start_state = `InfectionState::Exposed`,
		ProtectionEvent	latest_protection = `{ProtectionType::NoProtection, TimePoint(0)}`,
		bool	detected = `false`
	)

Create an Infection for a single Person.

Draws a random infection course.

Parameters

[in,out]	rng	PersonalRandomNumberGenerator of the Person.
[in]	virus	Virus type of the Infection.
[in]	age	AgeGroup to determine the ViralLoad course.
[in]	params	Parameters of the Model.
[in]	init_date	Date of initializing the Infection.
[in]	init_state	[Default: InfectionState::Exposed] InfectionState at time of initializing the Infection.
[in]	latest_protection	[Default: {ProtectionType::NoProtection, TimePoint(0)}] The pair value of last ProtectionType (previous Infection/Vaccination) and TimePoint of that protection.
[in]	detected	[Default: false] If the Infection is detected.

◆ Infection() [2/3]

mio::abm::Infection::Infection	(	PersonalRandomNumberGenerator &	rng,
		VirusVariant	virus,
		AgeGroup	age,
		const Parameters &	params,
		TimePoint	init_date,
		InfectionState	init_state,
		const InitialInfectionStateDistribution &	init_state_dist,
		ProtectionEvent	latest_protection = `{ProtectionType::NoProtection, TimePoint(0)}`,
		bool	detected = `false`
	)

Create an Infection for a single Person with a time spent in the given initial state that is drawn from the given distribution.

Parameters

[in,out]	rng	PersonalRandomNumberGenerator of the Person.
[in]	virus	Virus type of the Infection.
[in]	age	AgeGroup to determine the ViralLoad course.
[in]	params	Parameters of the Model.
[in]	init_date	Date of initializing the Infection.
[in]	init_state	InfectionState at time of initializing the Infection.
[in]	init_state_dist	Distribution to draw the relative time spent in the initial state from. Values have to be within [0, 1].
[in]	latest_protection	The pair value of last ProtectionType (previous Infection/Vaccination) and TimePoint of that protection.
[in]	detected	If the Infection is detected.

◆ Infection() [3/3]

mio::abm::Infection::Infection ( )

privatedefault

Member Function Documentation

◆ calculate_death_probability()

ScalarType mio::abm::Infection::calculate_death_probability	(	AgeGroup	age,
		const Parameters &	params
	)		const

private

Calculate the overall death probability for the infection.

Parameters

[in]	age	AgeGroup of the Person.
[in]	params	Parameters of the Model.

Returns: The probability of death for this infection.

◆ default_serialize()

auto mio::abm::Infection::default_serialize ( )

inline

This method is used by the default serialization feature.

◆ draw_infection_course_backward()

TimePoint mio::abm::Infection::draw_infection_course_backward	(	PersonalRandomNumberGenerator &	rng,
		AgeGroup	age,
		const Parameters &	params,
		TimePoint	init_date,
		InfectionState	init_state
	)

private

Determine Infection course prior to the given InfectionState start_state.

From the start_state, a random path through the InfectionState tree is chosen backwards, until Susceptible is reached. For more detailed information, refer to draw_infection_course_forward.

Parameters

[in,out]	rng	PersonalRandomNumberGenerator of the Person.
[in]	age	AgeGroup of the person.
[in]	params	Parameters of the Model.
[in]	init_date	Date of initializing the Infection.
[in]	init_state	InfectionState at time of initializing the Infection.

Returns: The starting date of the Infection.

◆ draw_infection_course_forward()

void mio::abm::Infection::draw_infection_course_forward	(	PersonalRandomNumberGenerator &	rng,
		AgeGroup	age,
		const Parameters &	params,
		TimePoint	init_date,
		InfectionState	init_state,
		ProtectionEvent	latest_protection
	)

private

Determine Infection course subsequent to the given InfectionState start_state.

From the start_state, a random path through the InfectionState tree is chosen, that is Susceptible -> InfectedNoSymptoms, InfectedNoSymptoms -> InfectedSymptoms or InfectedNoSymptoms -> Recovered, InfectedSymptoms -> Infected_Severe or InfectedSymptoms -> Recovered, InfectedSevere -> InfectedCritical or InfectedSevere -> Recovered or InfectedSevere -> Dead, InfectedCritical -> Recovered or InfectedCritical -> Dead, until either Recoverd or Dead is reached. The duration in each InfectionState is taken from the respective parameter.

Parameters

[in,out]	rng	PersonalRandomNumberGenerator of the Person.
[in]	age	AgeGroup of the Person.
[in]	params	Parameters of the Model.
[in]	init_date	Date of initializing the Infection.
[in]	init_state	InfectionState at time of initializing the Infection.
[in]	latest_protection	Latest protection against Infection, has an influence on transition probabilities.

◆ get_backward_transition()

StateTransition mio::abm::Infection::get_backward_transition	(	PersonalRandomNumberGenerator &	rng,
		AgeGroup	age,
		const Parameters &	params,
		InfectionState	current_state
	)		const

private

Get the backward transition from a given infection state.

Parameters

[in,out]	rng	PersonalRandomNumberGenerator of the Person.
[in]	age	AgeGroup of the Person.
[in]	params	Parameters of the Model.
[in]	current_state	Current infection state.

Returns: StateTransition representing the previous transition.

◆ get_dead_backward_transition()

StateTransition mio::abm::Infection::get_dead_backward_transition	(	PersonalRandomNumberGenerator &	rng,
		AgeGroup	age,
		const Parameters &	params
	)		const

private

Get the backward transition from dead state.

Parameters

[in,out]	rng	PersonalRandomNumberGenerator of the Person.
[in]	age	AgeGroup of the Person.
[in]	params	Parameters of the Model.

Returns: StateTransition representing the transition that led to death.

◆ get_forward_transition()

StateTransition mio::abm::Infection::get_forward_transition	(	PersonalRandomNumberGenerator &	rng,
		AgeGroup	age,
		const Parameters &	params,
		InfectionState	current_state,
		TimePoint	current_time,
		ProtectionEvent	latest_protection
	)		const

private

Get the forward transition from a given infection state.

Parameters

[in,out]	rng	PersonalRandomNumberGenerator of the Person.
[in]	age	AgeGroup of the Person.
[in]	params	Parameters of the Model.
[in]	current_state	Current infection state.
[in]	current_time	Current time point.
[in]	latest_protection	Latest protection against Infection.

Returns: StateTransition representing the next transition.

◆ get_infection_state()

InfectionState mio::abm::Infection::get_infection_state ( TimePoint t ) const

Get the InfectionState of the Infection.

Parameters

[in] t TimePoint of the querry.

Returns: InfectionState at the given TimePoint.

◆ get_recovered_backward_transition()

StateTransition mio::abm::Infection::get_recovered_backward_transition	(	PersonalRandomNumberGenerator &	rng,
		AgeGroup	age,
		const Parameters &	params
	)		const

private

Get the backward transition from recovered state.

Parameters

[in,out]	rng	PersonalRandomNumberGenerator of the Person.
[in]	age	AgeGroup of the Person.
[in]	params	Parameters of the Model.

Returns: StateTransition representing the transition that led to recovery.

◆ get_severity_protection_factor()

ScalarType mio::abm::Infection::get_severity_protection_factor	(	const Parameters &	params,
		ProtectionEvent	latest_protection,
		AgeGroup	age,
		TimePoint	current_time
	)		const

private

Get the severity protection factor based on latest protection.

Parameters

[in]	params	Parameters of the Model.
[in]	latest_protection	Latest protection against Infection.
[in]	age	AgeGroup of the Person.
[in]	current_time	Current time point.

Returns: The protection factor against severe outcomes.

◆ get_start_date()

TimePoint mio::abm::Infection::get_start_date ( ) const

Returns: Get the start date of the infection.

◆ get_viral_load()

ScalarType mio::abm::Infection::get_viral_load ( TimePoint t ) const

Gets the ViralLoad of the Infection at a given TimePoint.

Parameters

[in] t TimePoint of querry.

◆ get_viral_shed()

ScalarType mio::abm::Infection::get_viral_shed ( TimePoint t ) const

Get viral shed at a specific time.

Computed depending on current ViralLoad and individual invlogit function of each Person corresponding to https://www.science.org/doi/full/10.1126/science.abi5273 The mapping corresponds to Fig. 2 C. Formula of invlogit function can be found here: https://github.com/VirologyCharite/SARS-CoV-2-VL-paper/tree/main in ExtendedMethods.html, Section 3.1.2.1.

Also in accordance to Fig. 3d of another publication: https://www.nature.com/articles/s41564-022-01105-z/figures/3 The result is in arbitrary units and has to be scaled to the rate "infections per day".
Parameters

[in] t TimePoint of the querry.

Returns
Viral shed at given TimePoint.

◆ get_virus_variant()

VirusVariant mio::abm::Infection::get_virus_variant ( ) const

: Get VirusVariant.

Returns: VirusVariant of the Infection.

◆ initialize_viral_load()

void mio::abm::Infection::initialize_viral_load	(	PersonalRandomNumberGenerator &	rng,
		VirusVariant	virus,
		AgeGroup	age,
		const Parameters &	params,
		ProtectionEvent	latest_protection
	)

private

Initialize the viral load parameters for the infection.

Parameters

[in,out]	rng	PersonalRandomNumberGenerator of the Person.
[in]	virus	Virus type of the Infection.
[in]	age	AgeGroup of the Person.
[in]	params	Parameters of the Model.
[in]	latest_protection	Latest protection against Infection.

◆ initialize_viral_shed()

void mio::abm::Infection::initialize_viral_shed	(	PersonalRandomNumberGenerator &	rng,
		VirusVariant	virus,
		AgeGroup	age,
		const Parameters &	params
	)

private

Initialize the viral shed parameters and individual factor for the infection.

Parameters

[in,out]	rng	PersonalRandomNumberGenerator of the Person.
[in]	virus	Virus type of the Infection.
[in]	age	AgeGroup of the Person.
[in]	params	Parameters of the Model.

◆ is_detected()

bool mio::abm::Infection::is_detected ( ) const

Returns: Get the detected state.

◆ set_detected()

void mio::abm::Infection::set_detected ( )

Set the Infection to detected.

Member Data Documentation

◆ DefaultFactory< Infection >

friend mio::abm::Infection::DefaultFactory< Infection >

private

◆ m_detected

bool mio::abm::Infection::m_detected

private

Whether an Infection is detected or not.

◆ m_individual_viral_shed_factor

ScalarType mio::abm::Infection::m_individual_viral_shed_factor

private

Individual viral shed factor.

◆ m_infection_course

std::vector<std::pair<TimePoint, InfectionState> > mio::abm::Infection::m_infection_course

private

Start date of each InfectionState.

◆ m_log_norm_alpha

ScalarType mio::abm::Infection::m_log_norm_alpha

private

◆ m_log_norm_beta

ScalarType mio::abm::Infection::m_log_norm_beta

private

Parameters for the viral shed mapping, which is modelled through an invlogit function.

◆ m_viral_load

ViralLoad mio::abm::Infection::m_viral_load

private

ViralLoad of the Infection.

◆ m_virus_variant

VirusVariant mio::abm::Infection::m_virus_variant

private

Variant of the Infection.

Infection Class Reference

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ Infection() [1/3]

◆ Infection() [2/3]

◆ Infection() [3/3]

Member Function Documentation

◆ calculate_death_probability()

◆ default_serialize()

◆ draw_infection_course_backward()

◆ draw_infection_course_forward()

◆ get_backward_transition()

◆ get_dead_backward_transition()

◆ get_forward_transition()

◆ get_infection_state()

◆ get_recovered_backward_transition()

◆ get_severity_protection_factor()

◆ get_start_date()

◆ get_viral_load()

◆ get_viral_shed()

◆ get_virus_variant()

◆ initialize_viral_load()

◆ initialize_viral_shed()

◆ is_detected()

◆ set_detected()

Member Data Documentation

◆ DefaultFactory< Infection >

◆ m_detected

◆ m_individual_viral_shed_factor

◆ m_infection_course

◆ m_log_norm_alpha

◆ m_log_norm_beta

◆ m_viral_load

◆ m_virus_variant